[gmx-users] Fwd: LJ cut-offs

[Dawid das]

Since I join this discussion, this is perhaps a good moment to ask
following questions.
I use Gromacs 5.0.4 and the file.mdp options that I found here
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM , so:

1. The bug that was described here
https://github.com/NMRLipids/NmrLipidsCholXray/issues/4
does not apply to my case if I used only CPUs, LJ for vdW and PME for
electrostatics but I did use
default -tunepme (I guess it does not apply then as far as I understand the
manual). I just want to
make sure that my calculations are correct.

2. With the above setting in my *.log file there is line saying

Changing nstlist from 10 to 25, rlist from 1.2 to 1.235

and this is because verlet-buffer-tolerance sets the rlist. Is that OK?

Dawid

2017-01-11 19:34 GMT+01:00 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
:

> I found these two links from other post of mine which might be useful for
> this discussion too:
>
> People have used 11-12 switching range as well. So, if it works, there is
> no restriction to not choose such numbers with 0.1 nm difference in
> cutoffs.
>
> http://pubs.acs.org/doi/abs/10.1021/jp101759q
>
>
> There is a great discussion which is relevant and better to read.
>
> https://github.com/NMRLipids/NmrLipidsCholXray/issues/4
>
> Cheers
> Mohsen
>
> On Wed, Jan 11, 2017 at 10:46 AM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
> > Hi Guys,
> >
> > Thanks for your comments. My question was exactly what Dawid clarified.
> > Sure, I will read those as you suggested.
> >
> > Dawid, regarding this:
> > "You need to keep in mind however that each force field was optimized for
> > given set of cut-offs and
> > they virtually become part of that FF (just like FF formula and
> > parameters), so it is strongly recommended
> > not to change them"
> >
> > I agree. BUT, using charmm36 in gromacs or other software requires to
> > change some critical parameters like cut-offs to get a better agreements
> > with experiments as well as with simulations done with charmm/NAMD.
> > This is why.
> >
> > Cheers
> > Mohsen
> >
> > On Wed, Jan 11, 2017 at 5:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 1/10/17 10:40 PM, Mohsen Ramezanpour wrote:
> >>
> >>> Dear gromacs users,
> >>>
> >>> Please let me know your opinion on the following question:
> >>> Thanks in advance for your comments
> >>>
> >>>
> >> dx.doi.org/10.1002/jcc.21287
> >>
> >> While that paper (obviously) focuses on CHARMM, there is a vast amount
> of
> >> general MD information described in it, as well as cited literature.
> The
> >> section on nonbonded interactions probably addresses most of what you
> want
> >> to know.
> >>
> >> -Justin
> >>
> >>
> >>> ---------- Forwarded message ----------
> >>> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> >>> Date: Thu, Jan 5, 2017 at 5:20 PM
> >>> Subject: LJ cut-offs
> >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>>
> >>>
> >>> Dear Gromacs users,
> >>>
> >>> Every force field has been parametrized with a specific LJ cut-off
> which
> >>> must be the same for simulations using that force field.
> >>> However, I was wondering if there is any reason why people usually take
> >>> even numbers (e.g. 8-10, 8-12, 10-12 all with a difference of 2) for LJ
> >>> cut-offs in force field development?
> >>> Is there any rule that prohibit the use of 9-10, 9-11, or 11-12 for LJ
> >>> cut-off?
> >>>
> >>> Thanks
> >>>
> >>> Cheers
> >>> Mohsen
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >>
> >> --
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> >
> >
> >
> > --
> > *Rewards work better than punishment ...*
> >
>
>
>
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